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- PDB-4c9j: Structure of yeast mitochondrial ADP/ATP carrier isoform 3 inhibi... -

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Basic information

Entry
Database: PDB / ID: 4c9j
TitleStructure of yeast mitochondrial ADP/ATP carrier isoform 3 inhibited by carboxyatractyloside (P212121 crystal form)
ComponentsADP, ATP CARRIER PROTEIN 3
KeywordsTRANSPORT PROTEIN / MITOCHONDRIAL CARRIER
Function / homology
Function and homology information


Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / mitochondrial ADP transmembrane transport / Mitochondrial protein import / ATP:ADP antiporter activity / mitochondrial ATP transmembrane transport / heme transport / Mitochondrial protein degradation / anaerobic respiration / transmembrane transport / mitochondrial inner membrane ...Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / mitochondrial ADP transmembrane transport / Mitochondrial protein import / ATP:ADP antiporter activity / mitochondrial ATP transmembrane transport / heme transport / Mitochondrial protein degradation / anaerobic respiration / transmembrane transport / mitochondrial inner membrane / mitochondrion / identical protein binding
Similarity search - Function
ADP/ATP carrier protein, eukaryotic type / Mitochondrial carrier fold / Mitochondrial carrier domain / Mitochondrial carrier protein / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile. / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
CARDIOLIPIN / Carboxyatractyloside / ADP,ATP carrier protein 3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.397 Å
AuthorsRuprecht, J.J. / Hellawell, A.M. / Harding, M. / Crichton, P.G. / McCoy, A.J. / Kunji, E.R.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structures of Yeast Mitochondrial Adp/ATP Carriers Support a Domain-Based Alternating-Access Transport Mechanism
Authors: Ruprecht, J.J. / Hellawell, A.M. / Harding, M. / Crichton, P.G. / Mccoy, A.J. / Kunji, E.R.S.
History
DepositionOct 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP, ATP CARRIER PROTEIN 3
B: ADP, ATP CARRIER PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,83810
Polymers70,5122
Non-polymers10,3268
Water00
1
A: ADP, ATP CARRIER PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4195
Polymers35,2561
Non-polymers5,1634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP, ATP CARRIER PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4195
Polymers35,2561
Non-polymers5,1634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.286, 104.168, 154.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99751, -0.06649, -0.02351), (-0.06332, -0.99116, 0.11656), (-0.03105, -0.11478, -0.99291)
Vector: -8.40705, -22.94266, 353.53979)

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Components

#1: Protein ADP, ATP CARRIER PROTEIN 3 / ADP-ATP CARRIER ISOFORM 3 / ADP/ATP TRANSLOCASE 3 / ADENINE NUCLEOTIDE TRANSLOCATOR 3 / ANT 3


Mass: 35255.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): WB12 / References: UniProt: P18238
#2: Chemical ChemComp-CXT / Carboxyatractyloside


Mass: 770.816 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O18S2
#3: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.8 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1M TRIS PH 8.5, 20MM SODIUM CITRATE, 10% T-BUTANOL, 28% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.4→49.34 Å / Num. obs: 9455 / % possible obs: 99.2 % / Observed criterion σ(I): 6 / Redundancy: 3.9 % / Biso Wilson estimate: 52.23 Å2 / Rmerge(I) obs: 0.25 / Net I/σ(I): 5.9
Reflection shellResolution: 3.4→3.67 Å / Redundancy: 4 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.1 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C9G

4c9g


Resolution: 3.397→38.977 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 29.23 / Stereochemistry target values: ML
Details: RESIDUES 151-155 AND 205-219 OF CHAIN A, AND 152-155 AND 204-219 OF CHAIN B, ARE UNMODELLED OWING TO POOR DENSITY
RfactorNum. reflection% reflection
Rfree0.2969 443 4.7 %
Rwork0.2495 --
obs0.2518 9415 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.397→38.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 346 0 4413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024485
X-RAY DIFFRACTIONf_angle_d0.8276058
X-RAY DIFFRACTIONf_dihedral_angle_d16.9681681
X-RAY DIFFRACTIONf_chiral_restr0.043681
X-RAY DIFFRACTIONf_plane_restr0.002731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3975-3.88870.29311420.23882873X-RAY DIFFRACTION98
3.8887-4.89790.25321420.23152990X-RAY DIFFRACTION100
4.8979-38.97950.33781590.27423109X-RAY DIFFRACTION99

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